Genetic structure and linkage disequilibrium in landrace populations of barley in Sardinia

Theoretical and Applied Genetics

Volumn 125, Issue 1, 2012, Pages 171-184

  Rodriguez, Monica ^a   Rau, Domenico ^a   O'Sullivan, Donal ^b   Brown, Anthony H D ^c   Papa, Roberto ^d,e   Attene, Giovanna ^a  

^a UNIVERSITY OF SASSARI   (Italy)

^b NATIONAL INSTITUTE OF AGRICULTURAL BOTANY   (United Kingdom)

^c CSIRO   (Australia)

^d UNIVERSITÀ POLITECNICA DELLE MARCHE   (Italy)

^e ISTITUTO NAZIONALE DELLA NUTRIZIONE   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

AGRONOMY; CHROMOSOMES;

ANALYSIS OF MOLECULAR VARIANCES; DIVERSIFYING SELECTIONS; GEOGRAPHIC PATTERN; LINKAGE DISEQUILIBRIUM; NATURAL POPULATION; POLYMORPHISM MARKERS; POPULATION STRUCTURES; STRUCTURE ANALYSIS;

GENETIC ENGINEERING;

HORDEUM; HORDEUM VULGARE; HORDEUM VULGARE SUBSP. SPONTANEUM;

EID: 84864467196     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-012-1824-8     Document Type: Article

References (73)

1. Abdel-Ghani AH, Parzies HK, Omary A, Geiger HH (2004) Estimating the outcrossing rate of barley landraces and wild barley populations collected from ecologically different regions of Jordan. Theor Appl Genet 109: 588-595.
2. Agapow PM, Burt A (2001) Indices of multilocus linkage disequilibrium. Mol Ecol Notes 1: 101-102.
3. Allard RW (1999) History of plant population genetics. Annu Rev Genet 33: 1-27.
4. Attene G, Ceccarelli S, Papa R (1996) The barley (Hordeum vulgare L.) of Sardinia, Italy. Genet Resour Crop Evol 43: 385-393.
5. Bitocchi E, Nanni L, Rossi M, Bellucci E, Giardini A, Buonamici A, Vendramin GG et al (2009) Introgression from modern hybrid varieties into landrace populations of maize (Zea mays ssp. mays L.) in central Italy. Mol Ecol 18: 603-621.
6. Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23: 2633-2635.
7. Breseghello F, Sorrells ME (2006) Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 172: 1165-1177.
8. Briggs DE (1978) Barley. Chapman and Hall, London.
9. Brown AHD (2000) The genetic structure of crop landraces and the challenge to conserve them in situ on farms. In: Brush SB (ed) GENES in the FIELD. On-farm conservation of crop diversity. IPGRI/IDRC/Lewis Publishers, Boca Raton, pp 19-48.
10. Brown AHD, Feldman MW (1981) Population structure of multilocus associations. Proc Natl Acad Sci USA 78: 5913-5916.
11. Brown AHD, Feldman MW, Nevo E (1980) Multilocus structure in natural populations of Hordeum spontaneum. Genetics 96: 523-536.
12. Brush SB (2000) The issues of in situ conservation of crop genetic resources. In: Brush SB (ed) GENES in the FIELD. On-farm conservation of crop diversity. IPGRI/IDRC/Lewis Publishers, Boca Raton, pp 3-26.
13. Caldwell KS, Russell J, Langridge P, Powell W (2006) Extreme population dependent linkage disequilibrium detected in an inbreeding plant species, Hordeum vulgare. Genetics 172: 557-567.
14. Ceccarelli S, Grando S (2000) Barley landraces from the Fertile Crescent: a lesson for plant breeders. In: Brush SB (ed) GENES in the FIELD. On-farm conservation of crop diversity. IPGRI/IDRC/Lewis Publishers, Boca Raton, pp 3-26.
15. Charlesworth B, Sniegowski P, Stephan W (1994) The evolutionary dynamics of repetitive DNA in eukaryotes. Nature 371: 215-220.
16. Cockram J, White J, Leigh FJ, Lea VJ, Chiapparino E, Laurie DA, Meckay IJ, Powell W, O'Sullivan DM (2008) Association mapping of partitioning loci in barley. BMC Genet 9: 16. doi: 10. 1186/1471-2156-9-16.
17. Comadran J, Thomas WTB, van Eeuwijk FA, Ceccarelli S, Grando S, Stanca AM, Pecchioni N, Akar T, Al-Yassin A, Benbelkacem A, Ouabbou H, Bort J, Romagosa I, Hackett CA, Russell JR (2009) Patterns of genetic diversity and linkage disequilibrium in a highly structured Hordeum vulgare association-mapping population for the Mediterranean basin. Theor Appl Genet 119: 175-187.
18. Comadran J, Ramsay L, MacKenzie K, Hayes P, Close TJ, Muehlbauer G, Stein N, Waugh R (2011) Patterns of polymorphism and linkage disequilibrium in cultivated barley. Theor Appl Genet 122: 523-531. doi: 10. 1007/s00122-010-1466-7.
19. Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19: 11-15.
20. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14: 2611-2620.
21. Excoffier L, Lischer HEL (2010) Arlequin suite ver 3. 5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10: 564-567.
22. Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164: 1567-1587.
23. Falush D, Stephens M, Pritchard JK (2007) Inference of population structure using multilocus genotype data: dominant markers and null alleles. Mol Ecol Notes. doi: 10. 1111/j. 1471-8286. 2007. 01758. x.
24. Flint-Garcia SA, Thornsberry JM, Buckler ES (2003) Structure of linkage disequilibrium in plants. Annu Rev Plant Biol 54: 357-374.
25. Frankel OH, Brown AHD, Burdon JJ (1995) The conservation of plant biodiversity. Cambridge University Press, Cambridge.
26. Fu HH, Zheng ZW, Dooner HK (2002) Recombination rates between adjacent genic and retrotransposon regions in maize vary by 2 orders of magnitude. Proc Natl Acad Sci USA 99: 1082-1087.
27. Gao H, Williamson S, Bustamante CD (2007) An MCMC approach for joint inference of population structure and inbreeding rates from multi-locus genotype data. Genetics 176: 1635-1651.
28. Gaut BS, Long AD (2003) The lowdown on linkage disequilibrium. Plant Cell 15: 1502-1506.
29. Gorham J, Papa R, Aloy-Lleonart M (1994) Varietal differences in sodium uptake in barley cultivars exposed to soil salinity or salt spray. J Exp Bot 45: 895-901.
30. Guillot G, Leblois R, Coulon AL, Frantz AC (2009) Statistical methods in spatial genetics. Mol Ecol 18: 4734-4756.
31. Harlan JR (1975) Our vanishing genetic resources. Science 188: 618-621.
32. Hill WG, Robertson A (1968) Linkage disequilibrium in finite populations. Theor Appl Genet 38: 226-231.
33. Hubisz MJ, Falush D, Stephens M, Pritchard JK (2009) Inferring weak population structure with the assistance of sample group information. Mol Ecol Resour 9: 1322-1332.
34. Jaradat AA, Shahid M (2006) Population and multilocus isozyme structures in a barley landrace. Plant Genet Resour Charact Util 4: 108-116.
35. Kraakman ATW, Niks RE, van den Berg PMMM, Stam P, van Eeuwijk FA (2004) Linkage disequilibrium mapping of yield and yield stability in modern spring barley cultivars. Genetics 168: 435-446.
36. Landry PA, LaPointe FJ (1996) RAPD problems in phylogenetics. Zool Scr 25: 283-290.
37. Leigh F, Kalendar R, Lea V, Lee D, Donini P, Schulman AH (2003) Comparison of the utility of barley retrotransposon families for genetic analysis by molecular marker techniques. Mol Genet Genomics 269: 464-474.
38. Liu K, Goodman M, Muse S, Smith JS, Buckler E, Doebley J (2003) Genetic structure and diversity among maize inbred lines as inferred from DNA microsatellites. Genetics 165: 2117-2128.
39. Maccaferri M, Sanguineti MC, Noli E, Tuberosa R (2005) Population structure and long-range linkage disequilibrium in a durum wheat elite collection. Mol Breed 15: 271-289.
40. Mackay I, Powell W (2007) Methods for linkage disequilibrium mapping in crops. Trends Plant Sci 12: 57-63.
41. Malysheva-Otto LV, Ganal MW, Röder M (2006) Analysis of molecular diversity, population structure and linkage disequilibrium in a worldwide survey of cultivated barley germplasm (Hordeum vulgare L.). BMC Genet 7: 6.
42. Mather KA, Caicedo AL, Polato NR, Olsen KM, McCouch S, Purugganan MD (2007) The extent of linkage disequilibrium in rice (Oryza sativa L.). Genetics 177: 2223-2232.
43. Mazzucato A, Papa R, Bitocchi E, Mosconi P, Nanni L, Negri V, Picarella ME et al (2008) Genetic diversity, structure and marker-trait associations in a collection of Italian tomato (Solanum lycopersicum L.). Theor Appl Genet 116: 657-669.
44. Miller MP (1997) Tools for population genetic analysis (TFPGA) 1. 3: a Windows program for the analysis of allozyme and molecular population genetic data (distributed by the author).
45. Morrell PL, Toleno DM, Lundy KE, Clegg MT (2005) Low levels of linkage disequilibrium in wild barley (Hordeum vulgare ssp. spontaneum) despite high rates of self-fertilization. Proc Natl Acad Sci USA 102: 2442-2447.
46. Mueller JC (2004) Linkage disequilibrium for different scales and applications. Brief Bioinforma 5: 355-364.
47. Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89: 583-590.
48. Nevo E, Zohary D, Brown AHD, Haber M (1979) Genetic diversity and environmental associations of wild barley, Hordeum spontaneum, in Israel. Evolution 33: 815-833.
49. Papa R, Attene G, Barcaccia G, Ohgata A, Konishi T (1998) Genetic diversity in landrace populations of Hordeum vulgare L. from Sardinia, Italy, as revealed by RAPDs, isozymes and morphophenological traits. Plant Breed 117: 523-530.
50. Peakall R, Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6: 288-295.
51. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
52. Pusadee T, Jamjod S, Chiang Y, Rerkasem B, Schaal BA (2009) Genetic structure and isolation by distance in a landrace of Thai rice. Proc Natl Acad Sci USA 106: 13880-13885.
53. Queen RA, Gribbon BM, James C, Jack P, Flavell AJ (2004) Retrotransposon-based molecular markers for linkage and genetic diversity analysis in wheat. Mol Genet Genomics 271(1): 91-97. doi: 10. 1007/s00438-003-0960-x.
54. Remington DL, Thornsberry JM, Matsuoka Y, Wilson LM, Whitt SR et al (2001) Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proc Natl Acad Sci USA 98: 11479-11484.
55. Rodriguez M, O'Sullivan D, Donini P, Papa R, Chiapparino E, Leigh F, Attene G (2006) Integration of retrotransposon-based markers in a linkage map of barley. Mol Breed 17: 173-184.
56. Rodriguez M, Rau D, Papa R, Attene G (2008) Genotype by environment interactions in barley (Hordeum vulgare L.): different responses of landraces, recombinant inbred lines and varieties to Mediterranean environment. Euphytica 163: 231-247.
57. Rohlf FJ (2000) NTSYS-pc. Numerical taxonomy and multivariate analysis system, version 2. 1. Exeter Software, Setauket.
58. Rossi M, Bitocchi E, Bellucci E, Nanni L, Rau D, Attene G, Papa R (2009) Linkage disequilibrium and population structure in wild and domesticated populations of Phaseolus vulgaris L. Evol Appl 2: 504-522.
59. Rostoks N, Ramsay L, MacKenzie K, Cardle L, Bhat PR et al (2006) Recent history of artificial outcrossing facilitates whole-genome association mapping in elite inbred crop varieties. Proc Natl Acad Sci USA 103: 18656-18661.
60. Slatkin M (2008) Linkage disequilibrium: understanding the evolutionary past and mapping the medical future. Nat Rev Genet 9: 477-485.
61. Soleimani VD, Baum BR, Johnson DA (2007) Analysis of genetic diversity in barley cultivars reveals incongruence between S-SAP, SNP and pedigree data. Genet Resour Crop Evol 54: 83-97.
62. Song B-H, Windsor AJ, Schmid KJ, Ramos-Onsins S, Schranz ME et al (2009) Multilocus patterns of nucleotide diversity, population structure and linkage disequilibrium in Boechera stricta, a wild relative of Arabidopsis. Genetics 181: 1021-1033.
63. Spiegelhalter DJ, Best NG, Carlin BP, van der Linde A (2002) Bayesian measures of model complexity and fit. J R Stat Soc B 64: 583-640.
64. Tam SM, Mhiri C, Vogelaar A, Kerkveld M, Pearce SR, Grandbastien MA (2005) Comparative analyses of genetic diversities within tomato and pepper collections detected by retrotransposon-based S-SAP, AFLP and SSR. Theor Appl Genet 110: 819-831.
65. Tam SM, Causse M, Garcher C, Burck H, Mhiri C, Grandbastien M-A (2007) The distribution of copia-type retrotransposons and the evolutionary history of tomato and related wild species. J Evol Biol 20: 1056-1072.
66. Tanto Hadado T, Rau D, Bitocchi E, Papa R (2010) Adaptation and diversity along an altitudinal gradient in Ethiopian barley (Hordeum vulgare L.) landraces revealed by molecular analysis. BMC Plant Biol 10: 121.
67. Teshome A, Brown AHD, Hodgkin T (2001) Diversity in landraces of cereal and legume crops. Plant Breed Rev 21: 221-261.
68. Thomson MJ, Septiningsih EM, Suwardjo F, Santoso TJ, Silitonga TS, McCouch SR (2007) Genetic diversity analysis of traditional and improved Indonesian rice (Oryza sativa L.) germplasm using microsatellite markers. Theor Appl Genet 114(3): 559-568.
69. Vigouroux Y, McMullen M, Hittinger CT, Houchins K, Schulz L, Kresovich S, Matsuoka Y et al (2002) Identifying genes of agronomic importance in maize by screening microsatellites for evidence of selection during domestication. Proc Natl Acad Sci USA 99: 9650-9655.
70. Waugh R, Bonar N, Baird E, Thomas B, Graner A et al (1997a) Homology of AFLP products in three mapping populations of barley. Mol Gen Genet 255: 311-321.
71. Waugh R, McLean K, Flavell AJ, Pearce SR, Kumar A, Thomas BBT, Powell W (1997b) Genetic distribution of BARE-1-like retrotransposable elements in the barley genome revealed by sequence-specific amplification polymorphisms (S-SAP). Mol Gen Genet 253: 687-694.
72. Yeh FC, Yang R, Boyle T (1999) Popgene, version 1. 32. Microsoft window-based freeware for population genetic analysis. University of Alberta, Edmonton. http://www. ualberta. ca/~fyeh/index. htm.
73. Zhang LY, Marchand S, Tinker NA, Belzile F (2009) Population structure and linkage disequilibrium in barley assessed by DArT markers. Theor Appl Genet 119: 43-52.